Genome sequence of a food spoilage lactic acid bacterium, Leuconostoc gasicomitatum LMG 18811T, in association with specific spoilage reactions

Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses

Ribonucleoside hydrolases are enzymes that catalyze the cleavage of ribonucleosides to nitrogenous bases and ribose. These enzymes are found in many organisms: bacteria, archaea, protozoa, metazoans, yeasts, fungi and plants. Despite the simple reaction catalyzed by these enzymes, their physiological role in most organisms remains unclear. In this review, we compare the structure, kinetic parameters, physiological role, and potential applications of different types of ribonucleoside hydrolases discovered and isolated from different organisms.

Detection of Volatiles from Raw Beef Meat from Different Packaging Systems Using Solid-Phase Microextraction GC-Accurate Mass Spectrometry

The volatile profile of raw beef contains vital information related to meat quality and freshness. This qualitative study examines the effect of packaging system on the formation and release of volatile organic compounds (VOCs) from raw beef over time, relative to the packaging best before date (BBD). The three packaging systems investigated were modified atmospheric packaging, vacuum packaging, and cling-wrapped packaging. Porterhouse steak samples with the same BBD were analysed from 3 days before to 3 days after the BBD. VOCs were detected via preconcentration using solid-phase microextraction combined with gas chromatography–accurate mass quadrupole time-of-flight mass spectrometry. In total, 35 different VOCs were tentatively identified. Interestingly, there was no clear relationship of the VOCs detected between the three packaging systems, with only carbon disulphide and acetoin, both known volatiles of beef, detected in all three. This is the first study to investigate the effects of commercial packaging systems on VOC formation; it provides an understanding of the relationship of VOCs to the BBD that is essential for the development of on-pack freshness and quality sensors.

Characterization of the Psychrotrophic Lactic Acid Bacterium Leuconostoc gelidum subsp. aenigmaticum LS4 Isolated from Kimchi Based on Comparative Analyses of Its Genomic and Phenotypic Properties

With the aim of developing a new food starter culture, twenty-three psychrotrophic lactic acid bacteria (LAB) were isolated from 16 kimchi samples. One strain, Leuconostoc gelidum subsp. aenigmaticum LS4, which had typical psychrotrophic characteristics, was selected, and its phenotypic and genomic properties as a starter culture were investigated. The complete genome of L. aenigmaticum LS4 consisted of one circular chromosome (1,988,425 bp) and two plasmids (19,308 bp and 11,283 bp), with a guanine–cytosine content of 36.8%. L. aenigmaticum LS4 could grow at 5 °C but not at 37 °C, and maximum cell growth was obtained at 15~25 °C. L. aenigmaticum LS4 did not show any harmful characteristics such as hemolysis, undesirable enzyme activities, biogenic amine production, or antibiotic resistance. L. aenigmaticum LS4 was investigated for its suitability for technological processes (pH, temperature and NaCl treatment). L. aenigmaticum LS4 exhibited strong antimicrobial activity caused by the production of organic acids and bacteriocin, and it produced an exopolysaccharide composed of glucose with a molecular weight of 3.7 × 10⁶ Da. Furthermore, L. aenigmaticum LS4 improved the organoleptic qualities of kimchi juice. Our results indicate that L. aenigmaticum LS4 could be used as a functional starter culture for food (vegetable or fruit) fermentation at low temperatures.

Multilocus Sequence Typing of Leuconostoc mesenteroides Strains From the Qinghai-Tibet Plateau

Leuconostoc mesenteroides strains were a type of epiphytic bacterium widely used in fermented foods and products in the biochemical and pharmaceutical industries but data on its presence in foods from Qinghai-Tibet Plateau in China was scarce. In this study, molecular analysis based on multilocus sequence typing (MLST) with eight housekeeping genes (pyrG, groeL, rpoB, recA, uvrC, murC, carB, and pheS) was carried out on 45 L. mesenteroides strains isolated from different plants and dairy products from Qinghai-Tibet Plateau in China. The objective of this study was to perform genetic diversity analysis and explore the relationship between strains and isolate samples or separate regions. A total of 25 sequence types (STs) were identified with a diversity of up to 55.6%, which were grouped into one clonal complexes (CCs), 3 doublets and 17 singletons by eBURST. The results of minimum spanning tree and clustering analysis indicated these L. mesenteroides strains from the Qinghai-Tibet Plateau were relatively weakly related to the isolated region. However, there was a close relationship between the genotypes of L. mesenteroides strains and the type of the isolated sample, which was consistent with the results of API 50CH. The MLST scheme presented in this study provides a shareable and comparable sequence database and enhances our knowledge of the population diversity of L. mesenteroides strains which will be further used for the selection of industrial strains.

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

BACKGROUND

Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C.

RESULTS

We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures.

CONCLUSIONS

The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.

Longitudinal Metatranscriptomic Analysis of a Meat Spoilage Microbiome Detects Abundant Continued Fermentation and Environmental Stress Responses during Shelf Life and Beyond

Microbial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on one modified-atmosphere-packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and beyond. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive of the sensory quality of the beef: acceptable product (AP), early spoilage (ES), and late spoilage (LS). Both the 16S RNA taxonomic assignments from the total RNA and functional annotations of the active genes showed that these stages were significantly different from each other. However, the functional gene annotations showed more pronounced differences than the taxonomy assignments. Psychrotrophic lactic acid bacteria (LAB) formed the core of the SSO, according to the transcribed reads. Leuconostoc species were the most abundant active LAB throughout the study period, whereas the transcription activity of Streptococcaceae (mainly Lactococcus) increased after the product had spoiled. In the beginning of the experiment, the community managed environmental stress by cold-shock responses, which were followed by expression of the genes involved in managing oxidative stress. Glycolysis, the pentose phosphate pathway, and pyruvate metabolism were active throughout the study at a relatively stable level. However, the proportional transcription activities of the enzymes in these pathways changed over time.IMPORTANCE It is generally known which organisms are the typical SSO in foods, whereas the actively transcribed genes and pathways during microbial succession are poorly understood. This knowledge is important, since better approaches to food quality evaluation and shelf life determination are needed. Therefore, we conducted this study to find longitudinal markers that are connected to quality deterioration in a MAP beef product. This kind of RNA marker could be used to develop novel types of rapid quality analysis tools in the future. New tools are needed, since even though SSO can be detected and their concentrations determined using the current microbiological methods, results from these analyses cannot predict how close in time a spoilage community is to the production of clear sensory defects. The main reason for this is that the species composition of a spoilage community does not change dramatically during late shelf life, whereas the ongoing metabolic activities lead to the development of notable sensory deterioration.

Microbiomes in the Context of Refrigerated Raw Meat Spoilage

Meat spoilage is a complicated biological phenomenon taking place over the course of time. Several factors influence it, mainly external factors related to packaging and storage temperature but also internal ones related to contamination diversity and product ingredients. We conducted genomic studies of specific spoilage organisms (SSO) and investigated the spoilage microbiomes providing information about the factors that make a specific organism a competitive SSO, as well as the interactions between certain SSO and the most active species and pathways in packaged raw meat. Our studies showed that spoilage microbiomes are diverse, but certain aspects, such as oxygen content or added marinades, shape this diversity strongly. We have also characterized a new spoilage-associated pathway, i.e., heme-dependent respiration capability, in Leuconostoc gelidum subsp. gasicomitatum. The microbiome studies we conducted explain why this species has become a competitive SSO. It is a fast grower and gains advantage for its growth if oxygen is present in the packages. Since the contamination of psychrotrophic lactic acid bacteria is difficult to avoid in meat manufacture, leuconostocs cause spoilage problems from time to time especially in marinated products or those packaged under high-oxygen–containing atmospheres.

Production of Gamma-Aminobutyric Acid from Lactic Acid Bacteria: A Systematic Review

Gamma-aminobutyric acid (GABA) is widely distributed in nature and considered a potent bioactive compound with numerous and important physiological functions, such as anti-hypertensive and antidepressant activities. There is an ever-growing demand for GABA production in recent years. Lactic acid bacteria (LAB) are one of the most important GABA producers because of their food-grade nature and potential of producing GABA-rich functional foods directly. In this paper, the GABA-producing LAB species, the biosynthesis pathway of GABA by LAB, and the research progress of glutamate decarboxylase (GAD), the key enzyme of GABA biosynthesis, were reviewed. Furthermore, GABA production enhancement strategies are reviewed, from optimization of culture conditions and genetic engineering to physiology-oriented engineering approaches and co-culture methods. The advances in both the molecular mechanisms of GABA biosynthesis and the technologies of synthetic biology and genetic engineering will promote GABA production of LAB to meet people’s demand for GABA. The aim of the review is to provide an insight of microbial engineering for improved production of GABA by LAB in the future.

Quantitative Oxygen Consumption and Respiratory Activity of Meat Spoiling Bacteria Upon High Oxygen Modified Atmosphere

High oxygen modified atmosphere packaging is a commonly applied method to prolong the minimum shelf life of fresh (red) meats. Upon spoilage, changes of the initial oxygen concentration and microbiome composition can be observed. Thus, we classified the typical representative meat spoiling bacteria Brochothrix (B.) thermosphacta TMW2.2101 and the four lactic acid bacteria (LAB) Carnobacterium (C.) divergens TMW2.1577, C. maltaromaticum TMW2.1581, Leuconostoc (L.) gelidum subsp. gelidum TMW2.1618, and L. gelidum subsp. gasicomitatum TMW2.1619 along their oxygen consuming capacity, which can indicate the timeline of microbiome and sensorial changes. All bacteria were grown in a model system employing gas tight glass bottles containing meat simulation media and under modified atmosphere (70% O2 and 30% CO2). Oxygen concentrations of media and headspaces were monitored over time and the oxygen uptake rate (OUR) was calculated for all species. All bacteria were able to consume dissolved oxygen, with B. thermosphacta TMW2.2101 exhibiting a 31-times higher OUR per single cell in 60 h. Furthermore, all strains showed significant growth enhancement in the presence of heme indicating respiratory activity. Comparative genomic and physiological analyses predict the activity of a respiratory chain for all species upon high oxygen atmosphere. An additional cytochrome aa3 oxidase is suggested to be responsible for the increased OUR of B. thermosphacta TMW2.2101. Furthermore, B. thermosphacta TMW2.2101 revealed highest oxidative stress tolerance compared to the other bacteria, facilitating a higher respiratory activity. Coupling of respiration and fermentation via regeneration of NADH can be a competitive advantage for meat spoiling bacteria resulting in a higher cell count and possibly accelerated spoilage. The exhibited highest capacity for oxygen consumption of B. thermosphacta compared to LAB in vitro also suggests a higher contribution of this bacterium to the change in the atmosphere upon spoilage of MAP meats in situ.

Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition

Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities.IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.

Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis, Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas lundensis, and Weissella viridescens, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage

In this study, we present the draft genome sequences of nine strains from various psychrotrophic species identified in meat products and being recognized as important emerging food spoilers. Many of these species have only one or few strains being sequenced, and this work will contribute to the improvement of the overall genomic knowledge about them.

Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages

Leuconostoc gelidum subsp. gasicomitatum is a predominant lactic acid bacterium (LAB) in spoilage microbial communities of different kinds of modified-atmosphere packaged (MAP) food products. So far, only one genome sequence of a poultry-originating type strain of this bacterium (LMG 18811(T)) has been available. In the current study, we present the completely sequenced and functionally annotated genome of strain KG16-1 isolated from a vegetable-based product. In addition, six other vegetable-associated strains were sequenced to study possible "niche" specificity suggested by recent multilocus sequence typing. The genome of strain KG16-1 consisted of one circular chromosome and three plasmids, which together contained 2,035 CDSs. The chromosome carried at least three prophage regions and one of the plasmids encoded a galactan degradation cluster, which might provide a survival advantage in plant-related environments. The genome comparison with LMG 18811(T) and six other vegetable strains suggests no major differences between the meat- and vegetable-associated strains that would explain their "niche" specificity. Finally, the comparison with the genomes of other leuconostocs highlights the distribution of functionally interesting genes across the L. gelidum strains and the genus Leuconostoc.

Systems Biology of Microbial Exopolysaccharides Production

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

Packaging gas selects lactic acid bacterial communities on raw pork

AIMS

To study the effect of different CO2-rich packaging atmospheres on the composition of lactic acid bacterial communities proliferating on raw pork.

METHODS AND RESULTS

Raw pork loin was inoculated with a mixture of 14 lactic acid bacteria (LAB) strains previously associated with meat and packaged with four gas atmospheres: (i) 100% CO2 (ii) 80% N2 20% CO2 (iii) 80% N2, 20% CO2, 0·4% CO and (iv) 80% O2, 20% CO2. The colony counts of LAB, pH and composition of packaging gas were monitored every other day during the storage of 14 days at +6°C. The compositions of lactic acid bacterial communities on pork were evaluated after 7 days of storage with culture-independent, terminal restriction fragment length polymorphism analysis of 16S rRNA gene fragments. After 14 days of storage, the compositions of lactic acid bacterial communities were evaluated using identification of plate-grown LAB isolates by numerical ribopattern analysis. The results showed that (i) high concentration of CO2 in packaging atmosphere favoured Lactobacillus sp. (ii) high concentration of O2 favoured Leuconostoc spp. (iii) atmosphere with 80% N2, 20% CO2 favoured Lactococcus sp.

CONCLUSIONS

The composition of modified packaging atmosphere is a major factor selecting lactic acid bacterial communities proliferating on raw meat.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides an explanation for the compositions of lactic bacterial communities on modified atmosphere packaged raw meat observed in other studies. The results should be considered when attempting to manipulate LAB communities in raw meat, e.g. by protective cultures.

Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes

Previously, two riboswitch classes have been identified that sense and respond to the hypermodified nucleobase called prequeuosine1 (preQ1). The enormous expansion of available genomic DNA sequence data creates new opportunities to identify additional representatives of the known riboswitch classes and to discover novel classes. We conducted bioinformatics searches on microbial genomic DNA data sets to discover numerous additional examples belonging to the two previously known riboswitch classes for preQ1 (classes preQ1-I and preQ1-II), including some structural variants that further restrict ligand specificity. Additionally, we discovered a third preQ1-binding riboswitch class (preQ1-III) that is structurally distinct from previously known classes. These findings demonstrate that numerous organisms monitor the concentrations of this modified nucleobase by exploiting one or more riboswitch classes for this widespread compound.

Selection of bioprotective cultures for preventing cold-smoked salmon spoilage

Biopreservation is a natural technology of food preservation, which consists of inoculating food with microorganisms selected for their antibacterial properties. The objective of this study was to select lactic acid bacteria (LAB) to improve the quality of cold-smoked salmon (CSS). In this work, different strains representative of the 4 dominant species, identified in a previous study by pyrosequencing the 16S rRNA gene, were isolated and their spoiling potential in CSS blocks, sterilized by ionization, was assessed by twelve trained panelists along the vacuum storage at 8°C. Photobacterium phosphoreum, Brochothrix thermosphacta and Serratia proteamaculans released strong off-odors whereas the spoiling potential of Carnobacterium divergens was weaker. The spoiling capacity of Lactococcus piscium EU2241, Leuconostoc gelidum EU2247, Lactobacillus sakei EU2885, Staphylococcus equorum S030674 and 4 commercial starters was tested by the same method and 2 strains were eliminated due to off-odor production. The effect of the 6 selected LAB against the 4 specific spoiling organisms (SSOs) selected was tested by challenge tests in sterile CSS blocks. The protective effect of the LAB differed from one SSO to another and no correlation could be established between the sensory improvement, SSO inhibition, and the implantation or acidification of protective cultures (PCs). All the PCs except L. piscium reduced the off-odors released by P. phosphoreum although some of them had no effect on its growth. S. equorum, which did not grow in CSS, favored the implantation of P. phosphoreum but prevented its off-odor formation. L. piscium was the only strain that prevented the spoilage of B. thermosphacta and S. proteamaculans although it did not grow very well and did not acidify the product. L. gelidum EU2247 inhibited the growth of these 2 SSOs and lowered the pH but had no effect on the sensory quality. Finally, L. piscium was tested in 2 naturally contaminated products, with a positive effect on 1 batch. This effect was not correlated with the microbial ecosystem as determined by acultural and cultural techniques. Based on these results, the selection strategy is discussed.

Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi

Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.

Multilocus sequence typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic lactic acid bacterium causing spoilage of packaged perishable foods

Leuconostoc gelidum subsp. gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) that causes spoilage of a variety of modified-atmosphere-packaged (MAP) cold-stored food products. During the past 10 years, this spoilage organism has been increasingly reported in MAP meat and vegetable products in northern Europe. In the present study, the population structure within 252 L. gelidum subsp. gasicomitatum strains was determined based on a novel multilocus sequence-typing (MLST) scheme employing seven housekeeping genes. These strains had been isolated from meat and vegetable sources over a time span of 15 years, and all 68 previously detected pulsed-field gel electrophoresis (PFGE) genotypes were represented. A total of 46 sequence types (STs) were identified, with a majority of the strains (>60%) belonging to three major STs, which were grouped into three clonal complexes (CCs) and 17 singletons by Global Optimal eBURST (goeBURST). The results by Bayesian analysis of population structure (BAPS) mostly correlated with the grouping by goeBURST. Admixture analysis by BAPS indicated a very low level of exchange of genetic material between the subpopulations. Niche specificity was observed within the subpopulations: CC1 and BAPS cluster 1 consisted mostly of strains from a variety of MAP meats, whereas vegetable strains grouped together with strains from MAP poultry within CC2 and BAPS cluster 2. The MLST scheme presented in this study provides a shareable and continuously growing sequence database enabling global comparison of strains associated with spoilage cases. This will further advance our understanding of the microbial ecology of this industrially important LAB.

Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47

Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered.

Microbiota of regular sodium and sodium-reduced ready-to-eat meat products obtained from the retail market

The aim of this study was to assess the influence of sodium content on the microbiota on the surface of ready-to-eat (RTE) meat products purchased from the retail market in Canada. Products, including sliced and sausage-type deli meats, were analysed with culture-dependent and culture-independent methods. Bacteria were identified from 23 brands of products from different meat processors with claims of sodium content ranging from 390 to 1200 mg per 100 g of product. Out of 150 bacterial isolates, the most common were identified as Leuconostoc gelidum, Carnobacterium maltaromaticum, Brochothrix thermosphacta, and Leuconostoc gasicomitatum. Vacuum-packaged RTE deli sliced meat products had the largest population of bacteria. Leuconostocci were the most common isolates in this group of products, while carnobacteria were prevalent on products with moderate loads of bacteria. A higher incidence of carnobacteria and lower incidence of B. thermosphacta were detected on sodium-reduced products. Simpson’s and Shannon–Wiener indices showed that low sodium products (25%–50% less sodium) had an overall higher bacterial diversity. This was also observed when individual low sodium products were compared with their regular sodium counterpart.

Exploring the strain-specific attachment of Leuconostoc gelidum subsp. gasicomitatum on food contact surfaces

The psychrotrophic lactic acid bacterium (LAB) Leuconostoc gelidum subsp. gasicomitatum has emerged as one of the most prevalent specific spoilage organisms (SSOs) of packaged, cold-stored food products in Northern Europe. The whole genome sequencing of the type strain L. gelidum subsp. gasicomitatum LMG 18811(T) revealed genes encoding for proteins related to adhesion. In the present study the attachment of six food and environmental isolates was monitored on stainless steel (SS) and glass surfaces incubated (7 °C for 5-9 days) in two food simulating substrates (i.e. sweet bell pepper juice and boiled eggs in brine). The selection encompassed unique genotypes, isolated from different food products or sampling sites as well as slime-forming biotypes. The evaluation of the attached cells was performed with the bead vortexing method and a viability staining assay coupled with epifluorescence microscopy. On SS surfaces the slime-formers showed the lowest attachment (3.3-4.5 logCFU/cm(2)), while strain L. gelidum subsp. gasicomitatum ab2, which was isolated from an acetic acid bath in a vegetable salad company, reached significantly higher populations of attached cells exceeding 7 logCFU/cm(2). Strain ab2 formed dense cell aggregations on SS after 9 days of incubation in sweet bell pepper juice. The attachment ability of L. gelidum subsp. gasicomitatum on surfaces documented in the present study extends our knowledge and understanding of the spoilage potential and intra-subspecies diversity of this microbe.

Production of buttery-odor compounds and transcriptome response in Leuconostoc gelidum subsp. gasicomitatum LMG18811T during growth on various carbon sources

Leuconostoc gelidum subsp. gasicomitatum is a common spoilage bacterium in meat products packaged under oxygen-containing modified atmospheres. Buttery off-odors related to diacetyl/acetoin formation are frequently associated with the spoilage of these products. A whole-genome microarray study, together with gas chromatography (GC)-mass spectrometry (MS) analyses of the pathway end products, was performed to investigate the transcriptome response of L. gelidum subsp. gasicomitatum LMG18811(T) growing on semidefined media containing glucose, ribose, or inosine, which are essential carbon sources in meat. Generally, the gene expression patterns with ribose and inosine were quite similar, indicating that catabolism of ribose and nucleosides is closely linked. Diacetyl/acetoin concentrations as high as 110 or 470 μM were measured when growth was based on inosine or ribose, respectively. The gene expression results for pyruvate metabolism (upregulation of α-acetolactate synthase, downregulation of l-lactate dehydrogenase and pyruvate dehydrogenase) were as expected when diacetyl and acetoin were the end products. No diacetyl production (<7.5 μM) was detected with the glucose-containing medium, even though the cell counts of LMG18811(T) was 6 or 10 times higher than that on inosine or ribose, respectively. Although glucose was the most effective carbon source for the growth of L. gelidum subsp. gasicomitatum, utilization of inosine and ribose resulted in the production of the unwanted buttery-odor compounds. These results increase our understanding of which compounds are likely to enhance the formation of buttery odors during meat spoilage caused by L. gelidum subsp. gasicomitatum.

Functional genomics of lactic acid bacteria: from food to health

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

Significance of heme-based respiration in meat spoilage caused by Leuconostoc gasicomitatum

Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) which causes spoilage in cold-stored modified-atmosphere-packaged (MAP) meat products. In addition to the fermentative metabolism, L. gasicomitatum is able to respire when exogenous heme and oxygen are available. In this study, we investigated the respiration effects on growth rate, biomass, gene expression, and volatile organic compound (VOC) production in laboratory media and pork loin. The meat samples were evaluated by a sensory panel every second or third day for 29 days. We observed that functional respiration increased the growth (rate and yield) of L. gasicomitatum in laboratory media with added heme and in situ meat with endogenous heme. Respiration increased enormously (up to 2,600-fold) the accumulation of acetoin and diacetyl, which are buttery off-odor compounds in meat. Our transcriptome analyses showed that the gene expression patterns were quite similar, irrespective of whether respiration was turned off by excluding heme from the medium or mutating the cydB gene, which is essential in the respiratory chain. The respiration-based growth of L. gasicomitatum in meat was obtained in terms of population development and subsequent development of sensory characteristics. Respiration is thus a key factor explaining why L. gasicomitatum is so well adapted in high-oxygen packed meat.

Characterization and evaluation of the spoilage potential of Lactococcus piscium isolates from modified atmosphere packaged meat

A total of 222 psychrotrophic lactococci isolated from use-by day, modified atmosphere packaged (MAP) meat were identified to the species level by numerical analyses of EcoRI and ClaI ribopatterns and phylogenetic sequence analyses of 16S, rpoA and pheS genes. In addition, their meat spoilage potential was studied. The majority of the isolates (n=215) were identified as Lactococcus piscium, while seven isolates belonged to Lactococcus raffinolactis. L. piscium was shown to be adapted to growing in a variety of MAP meat products including broiler, turkey, pork, and minced meat from beef and pork, where they belonged to the predominating microbiota at the end of the storage. Numerical analyses of EcoRI and ClaI ribopatterns, and phylogenetic sequence analyses of rpoA and pheS genes were shown to be reliable tools in species level identification of meat lactococci. The spoilage potential of L. piscium was evaluated by inoculating representative isolates to MAP pork stored at 6 °C for 22 days. Development of spoilage population was monitored using a culture-independent T-RFLP approach. The sensory shelf life of pork inoculated with L. piscium was shortened compared to the uninoculated control. Alongside with the inoculated L. piscium isolates, Leuconostoc spp. present as initial contaminants in the samples thrived. This shows that even though lactococci were inoculated at higher levels compared to the natural microbiota, they did not occupy the niche and prevent the growth of other lactic acid bacteria.